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| rm align* angle* *.json *.pyidx *.png *.npy *.mp4 centroid* cluster* forces.txt gen_pairs.txt mean* min.dat sub* | ||
| rm -f align* angle* *.json *.pyidx *.png *.npy *.mp4 centroid* cluster* forces.txt gen_pairs.txt mean* min.dat sub* |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,175 +1,78 @@ | ||
| #!/bin/bash | ||
|
|
||
| echo "Testing align..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/align.py minitraj.dat aligned.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
|
|
||
| echo "" | ||
| echo "Testing oat" | ||
| echo "-----------" | ||
|
|
||
| echo "Testing backbone_flexibility..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/backbone_flexibility.py rna_tile.top minitraj.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| if [ $# -gt 0 ]; | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| PYTHON=$1 | ||
| else | ||
| echo "OK" | ||
| PYTHON="python" | ||
| fi | ||
|
|
||
| echo "" | ||
| test() { | ||
| tmpfile=$(mktemp) | ||
| $PYTHON $1 &> $tmpfile | ||
| local code_res=$? | ||
| grep_out=$(grep -i "ERROR" $tmpfile) | ||
| local grep_res=$? | ||
|
|
||
| echo "Testing bond_analysis..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/bond_analysis.py -p2 input_rna minitraj.dat pairs.txt 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
| if [ $code_res -eq 0 ] && [ $grep_res -eq 1 ] | ||
| then | ||
| echo " OK" | ||
| else | ||
| echo "" | ||
| echo $grep_out | ||
| echo "--> AN ERROR OCCURRED <--" | ||
| fi | ||
| } | ||
|
|
||
| echo "" | ||
| echo -n "Testing align..." | ||
| test "../src/oxDNA_analysis_tools/align.py minitraj.dat aligned.dat" | ||
|
|
||
| echo "Testing mean and deviations..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/mean.py -p 2 -d devs.json minitraj.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
| echo -n "Testing backbone_flexibility..." | ||
| test "../src/oxDNA_analysis_tools/backbone_flexibility.py rna_tile.top minitraj.dat" | ||
|
|
||
| echo "" | ||
| echo -n "Testing bond_analysis..." | ||
| test "../src/oxDNA_analysis_tools/bond_analysis.py -p2 input_rna minitraj.dat pairs.txt" | ||
|
|
||
| echo "Testing centroid with indexing..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/centroid.py -i index.txt mean.dat minitraj.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
| echo -n "Testing mean and deviations..." | ||
| test "../src/oxDNA_analysis_tools/mean.py -p 2 -d devs.json minitraj.dat" | ||
|
|
||
| echo "" | ||
| echo -n "Testing centroid with indexing..." | ||
| test "../src/oxDNA_analysis_tools/centroid.py -i index.txt mean.dat minitraj.dat" | ||
|
|
||
| echo "Testing contact_map..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/contact_map.py minitraj.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
| echo -n "Testing contact_map..." | ||
| test "../src/oxDNA_analysis_tools/contact_map.py minitraj.dat" | ||
|
|
||
| echo "" | ||
| echo -n "Testing distance and clustering (this one takes a while because of the plot)..." | ||
| test "../src/oxDNA_analysis_tools/distance.py -c -i minitraj.dat 1 3 5 67 34 56" | ||
|
|
||
| echo "Testing distance and clustering (this one takes a while because of the plot)..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/distance.py -c -i minitraj.dat 1 3 5 67 34 56 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
| echo -n "Testing duplex_finder..." | ||
| test "../src/oxDNA_analysis_tools/duplex_finder.py input_rna minitraj.dat" | ||
|
|
||
| echo "" | ||
| echo -n "Testing duplex_angle_plotter..." | ||
| test "../src/oxDNA_analysis_tools/duplex_angle_plotter.py -o angle.png -i angles.txt 7 37" | ||
|
|
||
| echo "Testing duplex_finder..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/duplex_finder.py input_rna minitraj.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
| echo -n "Testing generate_force..." | ||
| test "../src/oxDNA_analysis_tools/generate_force.py -f gen_pairs.txt input_rna minitraj.dat" | ||
|
|
||
| echo "" | ||
| echo -n "Testing minify..." | ||
| test "../src/oxDNA_analysis_tools/minify.py -a -d2 minitraj.dat min.dat" | ||
|
|
||
| echo "Testing duplex_angle_plotter..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/duplex_angle_plotter.py -o angle.png -i angles.txt 7 37 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
| echo -n "Testing multidimensional_scaling_mean..." | ||
| test "../src/oxDNA_analysis_tools/multidimensional_scaling_mean.py minitraj.dat -o meanM -d devsM" | ||
|
|
||
| echo "" | ||
| echo -n "Testing output_bonds..." | ||
| test "../src/oxDNA_analysis_tools/output_bonds.py -v energy.json input_rna minitraj.dat" | ||
|
|
||
| echo "Testing generate_force..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/generate_force.py -f gen_pairs.txt input_rna minitraj.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
| echo -n "Testing pca" | ||
| test "../src/oxDNA_analysis_tools/pca.py minitraj.dat mean.dat pca.json" | ||
|
|
||
| echo "" | ||
| echo -n "Testing subset_trajectory..." | ||
| test "../src/oxDNA_analysis_tools/subset_trajectory.py minitraj.dat rna_tile.top -i index.txt sub.dat" | ||
|
|
||
| echo "Testing minify..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/minify.py -a -d2 minitraj.dat min.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
|
|
||
| echo "" | ||
|
|
||
| echo "Testing multidimensional_scaling_mean..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/multidimensional_scaling_mean.py minitraj.dat -o meanM -d devsM 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
|
|
||
| echo "" | ||
|
|
||
| echo "Testing output_bonds..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/output_bonds.py -v energy.json input_rna minitraj.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
|
|
||
| echo "" | ||
|
|
||
| echo "Testing pca" | ||
| if | ||
| python ../src/oxDNA_analysis_tools/pca.py minitraj.dat mean.dat pca.json 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
|
|
||
| echo "Testing subset_trajectory..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/subset_trajectory.py minitraj.dat rna_tile.top -i index.txt sub.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
|
|
||
| echo "" | ||
|
|
||
| echo "Testing superimpose..." | ||
| if | ||
| python ../src/oxDNA_analysis_tools/superimpose.py mean.dat centroid.dat 2>&1 >/dev/null | grep -y "ERROR" | ||
| then | ||
| echo "AN ERROR OCCURED" | ||
| else | ||
| echo "OK" | ||
| fi | ||
| echo -n "Testing superimpose..." | ||
| test "../src/oxDNA_analysis_tools/superimpose.py mean.dat centroid.dat" | ||
|
|
||
| echo "" | ||
| echo "" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,15 @@ | ||
| Sphinx==3.4.1 | ||
| sphinx_rtd_theme==0.5.0 | ||
| myst_parser==0.17.2 | ||
| docutils==0.16 | ||
| Jinja2<3.1 | ||
| sphinx-argparse>=0.3.1 | ||
| ipython>=7.26.0 | ||
| Sphinx==7.0.1 | ||
| sphinx-argparse==0.3.2 | ||
| sphinx-rtd-theme==2.0.0 | ||
| sphinxcontrib-applehelp==1.0.2 | ||
| sphinxcontrib-bibtex==2.5.0 | ||
| sphinxcontrib-devhelp==1.0.2 | ||
| sphinxcontrib-htmlhelp==2.0.0 | ||
| sphinxcontrib-jquery==4.1 | ||
| sphinxcontrib-jsmath==1.0.1 | ||
| sphinxcontrib-qthelp==1.0.3 | ||
| sphinxcontrib-serializinghtml==1.1.5 | ||
| myst_parser==2.0.0 | ||
| docutils==0.20.1 | ||
| Jinja2==3.0.3 | ||
| ipython>=7.26.0 |
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